mmg_233_2013_genetics_genomicswikiaorg-20200214-history
Human Oral Microbiome Database
General Features Oral microbiome refers to the microrganisms that are found in human oral cavity and is strongly associated with periodontitis or extraoral infectious diseases. Human oral microbiome database (HOMD) is a database providing the taxonomy and genomics information of around 700 bacteria species of the microbiome 1. The database contains the taxonomy of human oral prokaryotes, a set of full-length 16S rRNA reference sequence, the dynamic genome annotation information and tools for sequence alignment. History The HOMD is started before the human microbiome project (HMP). The main goal of creating the database is to develop a systematic taxonomy for the unnamed oral microbes and create a database for the sequenced genomes of the microbes 2. The primary investigators of the Database are Tsute Chen, Floyd E. Dewhirst, Jacques Izard, Bruce J. Paster, Anne Tanner, and William G. Wade. This project is supported by grant R37 DE016937 from The National Institute for Dental and Craniofacial Research. Utility HOMD has a well-curated taxonomy of the oral bacteria in the database. The taxonomic hierarchy, detailed classification and links to the publications associated with the microbe are available in the HOMD Taxon Description page of the specific oral bacterium. An entire set of 16S rRNA is available for sequence alignment and can be downloaded from the database. The genome database of HOMD contains the stable or dynamic annotation of full, partial and meta genomic sequeces. Besides, the database also has tools such as BLAST for sequence alignment, KEGG for metabolic pathway and GO for gene ontology study. How is the database used? If we have a nucleotide sequence or amino acid sequence of a certain gene, we can find its homologous gene and its location in the whole genome or an operon in a certain oral microbe. 1. Goto HOMD (www.homd.org), click “taxa with annotated genomes” under the module Genome. 2. Click the “view genome” button of the bacteria species of your interest. 3. Click BLAST button of the specific strain that you are interested in. 4. Copy the amino acid sequence of the protein and paste it into the input box. In the drop out box, select blastp because we are aligning amino acid sequences, click search 5. Copy the ORF id (the string in the very left) and paste it into the box of “jump into the ORF ID”. 6. Click “go”, and the homologous gene is located. Research applications HOMD is used in different aspects of researches on microbes in oral or extraoral infections. D’Amato-Palumbo et al. utilized HOMD to determine whether a microorganism associated with vascular access-associated infections (VAIs) originated from oral cavity 3 . Then VAIs associated with bacteria are classified by whether or not the associated pathogens were found in HOMD. In another study to evaluate the salivary transcriptome, Spielmann et al. performed SOLiD sequencing to the cDNA library of saliva RNA, and aligned the whole transcriptome reads with HOMD and HOMF 16S rRNA RefSeq database 4. References 1. Chen, T., Yu, W-Han, Izard, J., Baranova, O.V., Lakshmanan, A., Dewhirst, F.E. (2010) The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database, Vol. 2010, Article ID baq013, doi: 10.1093/database/baq013 2. Dewhirst, F.E., Chen, T., Izard, J, Paster, B.J., Tanner, A.C.R., Yu, W.-H., Lakshmanan, A., Wade, W.G. (2010) The Human Oral Microbiome. J. Bacteriol. 192: 5002-5017. 3. D'Amato-Palumbo, S., A. A. Kaplan, et al. (2013). "Retrospective study of microorganisms associated with vascular access infections in hemodialysis patients. " Oral surgery, oral medicine, oral pathology and oral radiology 115(1): 56-61. 4. Spielmann, N., D. Ilsley, et al. (2012). "The Human Salivary RNA Transcriptome Revealed by Massively Parallel Sequencing. " Clinical Chemistry 58(9): 1314-1321.